load libraries
library(ggplot2)
library(data.table)
library(stringr)
library(dplyr)
library(tidyr)
library(rprojroot)
library(wesanderson)
Registered S3 method overwritten by 'wesanderson':
method from
print.palette nationalparkcolors
library(factoextra)
Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
library(FactoMineR)
library(nationalparkcolors)
library(cluster)
library(magrittr)
Attaching package: ‘magrittr’
The following object is masked from ‘package:tidyr’:
extract
library(NbClust)
library(clustree)
Loading required package: ggraph
set paths and filenames
### files
subset_table=sprintf("%s/intermediate_files/prev_SGBs_cluster_assignments_long_abundance.tsv",
find_rstudio_root_file())
metadata_table=sprintf("%s/data/some_teddy_MP142_metadata2.all_samples1.delivery.csv",
find_rstudio_root_file())
#iphop_table=sprintf("%s/data/TGVG_database_v1.1.exemplars.iphop_genus_outputs1.filt.csv",
# find_rstudio_root_file())
#long_table=sprintf("%s/data/mp142_TGVG1.1_MPA4_combined_abundance_table_longform1.tsv",
# find_rstudio_root_file())
get subset table
subset_dt <- fread(subset_table, header = T, sep = "\t")
species -> assignment labels
species_sub_dt <- subset_dt %>%
distinct(species, assignment)
make wider
subset_self_wide_dt <- subset_dt %>%
select(c(species, rounded_DOL, self_rel_abund)) %>%
pivot_wider(names_from = rounded_DOL,
values_from = self_rel_abund,
values_fill = 0)
species_l <- subset_self_wide_dt$species
subset_self_wide_dt <- subset_self_wide_dt %>% select(-species)
calc PCA
subset_prcomp1 <- prcomp(subset_self_wide_dt)
subset_PCA_dt <-as.data.frame(subset_prcomp1$x[,1:5])
setDT(subset_PCA_dt)
subset_PCA_dt$species <- species_l
subset_assign_PCA_dt <- merge(subset_PCA_dt, species_sub_dt,
by = "species")
plot PCA
subset_assign_PCA_dt %>%
ggplot(aes(x = PC1, y = PC2, color = assignment)) +
geom_point(alpa = 0.3) +
theme_bw()
Warning in geom_point(alpa = 0.3) :
Ignoring unknown parameters: `alpa`
calc tSNE
emb_bac <- Rtsne::Rtsne(subset_prcomp1$x[,1:10], perplexity = 30)
embb_bac <- as.data.frame(emb_bac$Y)
setDT(embb_bac)
embb_bac$species <- species_l
subset_assign_tSNE_dt <- merge(embb_bac, species_sub_dt,
by = "species")
#wes_palette("Darjeeling1", 8, type = "continuous")
pal <- park_palette("Arches")
coul <- colorRampPalette(pal)(8)
subset_tsne_p <- subset_assign_tSNE_dt %>%
ggplot(aes(x = V1, y = V2, fill = assignment)) +
geom_point(alpha = 0.85,
shape = 21,
color = "black",
size = 3) +
labs(x = "t-SNE 1",
y = "t-SNE 2") +
theme_bw() +
scale_fill_manual(values = coul)
subset_tsne_p
ggsave(
subset_tsne_p,
file = sprintf("%s/charts/temporal_subset_tsne1.pdf",
find_rstudio_root_file()),
width = 8, height= 5
)
check stats on PCA
subset_pca <- PCA(subset_self_wide_dt, graph = FALSE)
# Visualize eigenvalues/variances
fviz_screeplot(subset_pca, addlabels = TRUE, ylim = c(0, 41))
# Extract the results for variables
var <- get_pca_var(subset_pca)
# Contributions of variables to PC1
fviz_contrib(subset_pca, choice = "var", axes = 1, top = 10)
# Contributions of variables to PC2
fviz_contrib(subset_pca, choice = "var", axes = 2, top = 10)
# Control variable colors using their contributions to the principle axis
fviz_pca_var(subset_pca, col.var="contrib",
gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
repel = TRUE # Avoid text overlapping
) + theme_minimal() + ggtitle("Variables - PCA")
fviz_nbclust(subset_self_wide_dt, kmeans, method = "wss", k.max = 24) +
theme_minimal() +
ggtitle("the Elbow Method")
fviz_nbclust(subset_self_wide_dt, kmeans, method = "silhouette", k.max = 24) +
theme_minimal() +
ggtitle("The Silhouette Plot")
Warning: did not converge in 10 iterations
gap_stat <- clusGap(subset_self_wide_dt,
FUN = kmeans,
nstart = 30,
K.max = 24,
B = 50)
Clustering k = 1,2,..., K.max (= 24): ..
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done
Bootstrapping, b = 1,2,..., B (= 50) [one "." per sample]:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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. 50
fviz_gap_stat(gap_stat) +
theme_minimal() +
ggtitle("fviz_gap_stat: Gap Statistic")
kmean_calc <- function(df, ...){
kmeans(df, scaled = ..., nstart = 30)
}
km2 <- kmean_calc(subset_self_wide_dt, 2)
km3 <- kmean_calc(subset_self_wide_dt, 3)
km4 <- kmeans(subset_self_wide_dt, 4)
km5 <- kmeans(subset_self_wide_dt, 5)
km6 <- kmeans(subset_self_wide_dt, 6)
km7 <- kmeans(subset_self_wide_dt, 7)
km8 <- kmeans(subset_self_wide_dt, 8)
km9 <- kmeans(subset_self_wide_dt, 9)
km10 <- kmeans(subset_self_wide_dt, 10)
km11 <- kmeans(subset_self_wide_dt, 11)
p1 <- fviz_cluster(km2, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 2")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p2 <- fviz_cluster(km3, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 3")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p3 <- fviz_cluster(km4, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 4")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p4 <- fviz_cluster(km5, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 5")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p5 <- fviz_cluster(km6, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 6")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p6 <- fviz_cluster(km7, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 7")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p7 <- fviz_cluster(km8, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 8")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p8 <- fviz_cluster(km9, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 9")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p9 <- fviz_cluster(km10, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 10")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
p10 <- fviz_cluster(km11, data = subset_self_wide_dt,
frame.type = "convex",
labelsize = 0) + theme_minimal() +
ggtitle("k = 11")
Warning: argument frame is deprecated; please use ellipse instead.
Warning: argument frame.type is deprecated; please use ellipse.type instead.
cowplot::plot_grid(p1, p2, p3, p4, p5, p6, p7, p8, p9, p10,
labels = c("k2", "k3", "k4", "k5", "k6", "k7"))
ssc <- data.frame(
kmeans = c(2,3,4,5,6,7,8,9,10,11),
within_ss = c(mean(km2$withinss), mean(km3$withinss),
mean(km4$withinss), mean(km5$withinss),
mean(km6$withinss), mean(km7$withinss),
mean(km8$withinss), mean(km9$withinss),
mean(km10$withinss),mean(km11$withinss)),
between_ss = c(km2$betweenss, km3$betweenss, km4$betweenss,
km5$betweenss, km6$betweenss, km7$betweenss,
km8$betweenss, km9$betweenss, km10$betweenss,
km11$betweenss)
)
ssc %<>% gather(., key = "measurement", value = value, -kmeans)
#ssc$value <- log10(ssc$value)
ssc %>% ggplot(., aes(x=kmeans, y=log10(value), fill = measurement)) +
geom_bar(stat = "identity", position = "dodge") +
ggtitle("Cluster Model Comparison") +
xlab("Number of Clusters") +
ylab("Log10 Total Sum of Squares") +
scale_x_discrete(name = "Number of Clusters",
limits = c("0", "2", "3", "4", "5", "6",
"7", "8", "9", "10", "11"))
res.nbclust <- NbClust(subset_self_wide_dt, distance = "euclidean",
min.nc = 2, max.nc = 14,
method = "complete", index ="all")
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
Warning in log(det(P)/det(W)) : NaNs produced
*** : The Hubert index is a graphical method of determining the number of clusters.
In the plot of Hubert index, we seek a significant knee that corresponds to a
significant increase of the value of the measure i.e the significant peak in Hubert
index second differences plot.
*** : The D index is a graphical method of determining the number of clusters.
In the plot of D index, we seek a significant knee (the significant peak in Dindex
second differences plot) that corresponds to a significant increase of the value of
the measure.
*******************************************************************
* Among all indices:
* 7 proposed 2 as the best number of clusters
* 2 proposed 3 as the best number of clusters
* 3 proposed 5 as the best number of clusters
* 7 proposed 6 as the best number of clusters
* 1 proposed 10 as the best number of clusters
* 1 proposed 11 as the best number of clusters
* 1 proposed 12 as the best number of clusters
* 2 proposed 14 as the best number of clusters
***** Conclusion *****
* According to the majority rule, the best number of clusters is 2
*******************************************************************
tmp <- NULL
for (k in 1:11){
tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30)
}
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning: did not converge in 10 iterations
Warning: did not converge in 10 iterations
Warning: did not converge in 10 iterations
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
Warning in tmp[k] <- kmeans(subset_self_wide_dt, k, nstart = 30) :
number of items to replace is not a multiple of replacement length
df <- data.frame(tmp)# add a prefix to the column names
colnames(df) <- seq(1:11)
colnames(df) <- paste0("k",colnames(df))# get individual PCA
df.pca <- prcomp(df, center = TRUE, scale. = FALSE)
ind.coord <- df.pca$x
ind.coord <- ind.coord[,1:2]
df <- bind_cols(as.data.frame(df), as.data.frame(ind.coord))
clustree(df, prefix = "k")